The Sergipe River estuary has been subjected to a range of anthropogenic activities including food, plastic, textile, ceramic and metallurgical production plants along with domestic sewage inputs, all of which are of environmental concern. In this study, the levels of fecal coliforms (FC) in surface water samples and sterols in superficial sediment samples collected from the Sergipe River estuary were determined. Based on the FC concentrations, 58% of the water samples were considered Water Potentially Unusable (WPU) according to the United States Environmental Protection Agency (USEPA). Concentrations of coprostanol ranged from 13 to 1072 ng g−1, indicating a significant input of sewage at some points in the estuary. Principal Component Analysis (PCA) showed that there is no clear correlation between the coprostanol and coliform data, which may be due to the high resistance to degradation of coprostanol in sediments and to recent inputs of sewage at the water sample collection points. Display omitted •The distribution of sterols in sediments was compared to fecal coliforms in water samples.•High concentrations of coprostanol provided evidences of sewage contamination.•Diagnostic ratios between sterols enhanced the identification of sewage contamination.•PCA showed that there is no clear correlation between the coprostanol and coliforms.